<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@VERSION_STRING@.0">
    <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @home_dir@
        macs2 refinepeak
            -b '${ bed_infile }'
            -i '${ infile }'
            --format '${ infile.extension.upper() }'
            --cutoff '${ cutoff }'
            --window-size '${ winsize }'
            --ofile '${ outfile }'
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
        <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" />
        <param name="cutoff" type="float" label="Cutoff" value="5.0" help="default: 5.0 (--cutoff)"/>
        <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" />
    </inputs>

    <outputs>
        <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="refinepeak_bam_input.bam" ftype="bam"/>
            <param name="bed_infile" value="refinepeak_bed_input.bed" ftype="bed"/>
            <param name="cutoff" value="5.0"/>
            <param name="winsize" value="200"/>
            <output name="outfile" file="refinepeak_output.bed"/>
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**

This is **refinepeak** utility from the MACS2_ Package. It is an experimental utility that takes raw read alignments, refines peak summits and gives scores measuring balance of forward- backward tags. Inspired by the SPP_ pipeline.

.. _MACS2: https://github.com/taoliu/MACS
.. _SPP: http://compbio.med.harvard.edu/Supplements/ChIP-seq/

@citation@
]]>
    </help>
    <expand macro="citations" />
</tool>